Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

Jacob Sonne, Morten Østergaard Jensen, Flemming Y. Hansen, Lars Hemmingsen, Günther H. Peters

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

    Resumé

    Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.
    OriginalsprogEngelsk
    TidsskriftBiophysical Journal
    Vol/bind92
    Udgave nummer12
    Sider (fra-til)4157-4167
    Antal sider11
    ISSN0006-3495
    DOI
    StatusUdgivet - 2007

    Emneord

      Citer dette

      Sonne, Jacob ; Jensen, Morten Østergaard ; Hansen, Flemming Y. ; Hemmingsen, Lars ; Peters, Günther H. / Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. I: Biophysical Journal. 2007 ; Bind 92, Nr. 12. s. 4157-4167.
      @article{3fdaf8f0a40111dcaf2d000ea68e967b,
      title = "Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension",
      abstract = "Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 {\AA}2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 {\AA}2. Compared to the 48 {\AA}2, the new value of 60.4 {\AA}2 is in fair agreement with the experimental value of 64 {\AA}2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright {\circledC} 2007 by the Biophysical Society.",
      keywords = "ensemble, force field, lipid bilayers, molecular dynamics",
      author = "Jacob Sonne and Jensen, {Morten {\O}stergaard} and Hansen, {Flemming Y.} and Lars Hemmingsen and Peters, {G{\"u}nther H.}",
      year = "2007",
      doi = "10.1529/biophysj.106.087130",
      language = "English",
      volume = "92",
      pages = "4157--4167",
      journal = "Biophysical Journal",
      issn = "0006-3495",
      publisher = "Cell Press",
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      Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. / Sonne, Jacob; Jensen, Morten Østergaard; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

      I: Biophysical Journal, Bind 92, Nr. 12, 2007, s. 4157-4167.

      Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

      TY - JOUR

      T1 - Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

      AU - Sonne, Jacob

      AU - Jensen, Morten Østergaard

      AU - Hansen, Flemming Y.

      AU - Hemmingsen, Lars

      AU - Peters, Günther H.

      PY - 2007

      Y1 - 2007

      N2 - Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.

      AB - Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.

      KW - ensemble

      KW - force field

      KW - lipid bilayers

      KW - molecular dynamics

      U2 - 10.1529/biophysj.106.087130

      DO - 10.1529/biophysj.106.087130

      M3 - Journal article

      VL - 92

      SP - 4157

      EP - 4167

      JO - Biophysical Journal

      JF - Biophysical Journal

      SN - 0006-3495

      IS - 12

      ER -